SMTL ID : 5lfv.1 (1 other biounit)

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 7 residues within 4Å: Chain A: S.22, L.75, G.76, N.82, T.84, P.149, R.152 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.75, A:P.149 Hydrogen bonds: A:S.22

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.2: 4 residues within 4Å: Chain A: H.4, W.5, P.30, Y.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.5, A:W.5, A:Y.110

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.206 No protein-ligand interaction detected (PLIP) NAG.4: 7 residues within 4Å: Chain A: E.227, N.229, V.232, S.241, L.243, Y.272 Ligands: SO4.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.232 Hydrogen bonds: A:S.241, A:S.241, A:Y.272 Water bridges: A:S.241, A:S.241 NAG.5: 2 residues within 4Å: Chain A: Q.296, N.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.296, A:N.298

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: A.36, V.37, V.38, D.77, L.78, G.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.36, A:V.38, A:V.38, A:G.79

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: I.225, V.226, M.228, R.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.228 Salt bridges: A:R.299 SO4.8: 1 residues within 4Å: Chain A: R.60 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.60 SO4.9: 4 residues within 4Å: Chain A: A.134, T.190, R.191, Y.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.191 Salt bridges: A:R.191 SO4.10: 3 residues within 4Å: Chain A: N.229, S.230 Ligands: NAG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.229, A:S.230 Water bridges: A:S.230, A:S.230 SO4.11: 4 residues within 4Å: Chain A: S.11, T.12, H.115, V.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.11 Salt bridges: A:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Structural basis of myelin-associated glycoprotein adhesion and signalling. Nat Commun (2016)

Release Date

2016-12-14

Peptides

Myelin-associated glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myelin-associated glycoprotein

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